Plants can host a wide range of microbes, collectively known as the plant microbiome, in the rhizosphere (i.e., the region of soil in the vicinity of plant roots), endosphere (i.e., plant internal tissues), and phyllosphere (i.e., stem, leaves, or flowers) as illustrated in Figure 1 [24]. These microbiomes form long-lasting interactions with the host plant, leading to positive, neutral, or negative impacts on crop performance and microbe-mediated biogeochemical processes [25]. The microbial community that is beneficial to the host plant’s health, function, and evolution, are termed microsymbionts for forming a symbiotic relationship with the plant. The other type of microbe functions as plant pathogens, causing damage to the host plant. In most cases, the beneficial effects of microorganisms on plants are not caused by a single microbe, but rather by a consortium of different microorganisms that induce systemic resistance and promote plant growth [26]. Berendsen et al., reported the prevalence of three bacterial genera, Microbacterium, Stenotrophomonas, and Xanthomonas, in the rhizosphere of Arabidopsis thaliana when the foliar defense was activated by the downy mildew pathogen Hyaloperonospora arabidopsidis [27]. This study revealed that the plant recruited these bacterial species in the root zone to induce systemic resistance against downy mildew. Moreover, the formation of this symbiotic relationship in the primary population of downy mildew-infected plants resulted in a higher chance of survival of the second population of plants grown in the same soil. Microbiomes found in the endosphere and rhizosphere regions have also been shown to suppress plant diseases caused by fungal pathogens Gaeumannomyces graminis and Rhizoctonia solani (a soil-born pathogen) [28,29]. Similarly, other studies suggested the impact of a consortium of endophytes, including the fungi Rhodotorula graminis, and the bacteria Burkholderia vietnamiensis, Rahnella sp., Burkholderia sp., Acinetobacter calcoaceticus, Sphingomonas yanoikuyae, Pseudomonas sp., Rhizobium tropici, and Curtobacterium sp. on the enhanced drought stress tolerance in poplar plants [30]. In another study, pepper plants inoculated with desert-adapted bacteria displayed higher tolerance to water shortage compared with control plants. The bacteria enhanced the root biomass and length of plants (by 40%), which in turn improved the plant’s ability to uptake water and survive under water stress conditions [31]. Furthermore, mutualism between plants and microbes increases nutrient availability for plants. Beneficial interactions of the host plant with the microbial community contribute to the co-existence of multiple plant species, thereby enhancing plant and microbial diversity. The heterospecific plant-soil feedback responses play an important role in the co-existence of species, ecological succession, and species invasiveness. A meta-analysis conducted by Kutakova et al., suggest that plants grew better in soil conditioned by their closely related species than in soil conditioned by less frequently co-occurring species [32].

However, microbes that act as plant pathogens can directly infect the seedlings and suppress beneficial interactions. There are three main categories of pathogens: biotrophs, that feed on nutrients while keeping the host plant alive; necrotrophs, that suppress and destabilize the host’s immune system by producing tissue-degrading toxins and enzymes and feed on the dead tissue; and hemibiotrophs, that initially behave like biotrophs but the transition to necrotrophs in later stages of the disease [11]. For instance, Pseudomonas syringae (P. syringae) strains secrete the effector molecule, AvrPto1, which suppresses immune-related proteins in tomato plants. These effector molecules are specific to the pathogen [33].

The plant produces signaling hormones or phytohormones that include salicylic acid (SA), jasmonic acid (JA), ethylene (ET), abscisic acid (ABA), and auxins (such as indole-3-acetic acid (IAA)). The phytohormone signals are generated in the infected tissue and then circulated throughout the plant via the xylem and phloem. A progressive variation in the phytohormone levels serves as an early signal of plant stress [34,35,36]. Figure 2 shows a simplified model of the phytohormone dynamics in response to a stress condition [37]. SA, JA, ABA, and IAA are among the most important regulators of induced defense mechanisms [33,36,38,39,40,41,42,43]. Progressive variations in their levels have been reported in response to abiotic stressors including drought, salt, and cold/heat conditions [43,44,45,46] as well as biotic stressors including pathogen infection [47,48]. Exogenous application of these hormones is found to mitigate oxidative stress in plants [46,49,50,51,52,53,54,55]. Oxidative stress occurs due to a burst of reactive oxygen species, which are triggered by biotic (attack by microbes, pests, herbivores) and abiotic (drought/floods, temperature variations, soil nutrient/salinity/pH deficiencies) stresses. Root exudates are another form of signaling molecules that mediate the communication of plants with the rhizosphere. Root exudates are primarily composed of sugars, amino acids, organic acids, and vitamins, serving as a rich source of nutrients for the microbial community [56]. These exudates serve as carbon and energy sources for microorganisms living in the rhizosphere, while also profoundly influencing the composition and diversity of the microbial community [57]. Plants release the majority of photosynthates (the products of photosynthesis) into the rhizosphere through roots. Plants also release 100 teragrams (Tg) of methanol and 530 teragrams (Tg) of isoprene each year [58,59]. The interconnected signaling pathways of the compounds secreted from plants are central to the plant’s ability to fine-tune the rhizosphere’s microbiome structure or the induction of defenses in response to stressors. This section describes the various signaling molecules that mediate plant-microbial interactions.